Amino acids, Proteins & DNA (AQA A Level Chemistry)

Two amino acids, alanine and valine are drawn in Figure 1. 

Figure 1

  i) Give the IUPAC name for valine.

ii) Draw the species formed when alanine is in a solution of high pH.

i) When alanine and valine, drawn in Figure 1, react together a dipeptide is formed. Give the structured formula of two dipeptides which are formed when these two molecules react together.

ii) Give the formula of the molecule that is eliminated when these two amino acids

Name the type of reaction and the structural formula of alanine when it reacts with propanol, CH₃CH₂CH₂OH in the presence of concentrated sulphuric acid, H₂SO₄.

Valine exists as a pair of stereoisomers. 

Explain the meaning of the term stereoisomers and explain how the stereoisomers of valine can be distinguished from one another.

A student hydrolyses a dipeptide to form a solution containing a mixture of amino acids. This mixture is then analysed by silica gel thin-layer chromatography (TLC) using a toxic solvent. The individual amino acids are then identified from their Rf values.

Outline the main steps in producing the chromatogram that will enable the student to calculate the Rf values. Include any safety precautions that the student should take.

Thin Layer Chromatography is a commonly used analytical technique. Once a chromatogram has been produced, often an Rf value will be calculated.

i) Give the equation to which can be used to calculate Rf values.

ii) A chromatogram is shown in Figure 1. Calculate the Rf values for both compounds shown in the diagram. Give your answer to two decimal places.

 Figure 1

Explain why the amino acids in the solution have different Rf values.          

Give three advantages of Thin Layer Chromatography (TLC) as an analytical technique.

A section of a beta pleated sheet is shown in Figure 1. Explain how the interactions of the structure are formed.

Figure 1

A single strand of DNA is made from many nucleotides linked together. Draw the structure of the nucleotide that contains cytosine and name the three components. You will need to clearly show the bonding between the three different components. 

Complete Table 1 by placing a Y in the box that indicates which compound is involved in the process of making a protein or a strand of DNA. 

Table 1

Explain how the double helix structure of DNA is held together. In your answer you should make reference to the type of bonding and intermolecular forces that are present.

Use your data sheet to help you answer the following questions about amino acids,

i) Draw the zwitterion ion of lysine

ii) Give the IUPAC name of serine

iii) Draw the structural formula of the species formed by alanine at pH 1.

Cis-platin can act as an anti cancer drug. It works by attaching itself to DNA and not allowing it to function properly. Cis-platin and an isomer, trans-platin, are drawn in Figure 1 below. 

Figure 1 

i) Explain how cis platin is able to stop the growth of cancer cells.

ii) Suggest why trans-platin would not be able to do the same.

iii) Give one risk associated with taking cis-platin as an anti cancer drug

Naproxen is a drug used to treat pain from arthritis and is drawn in Figure 2. Drugs treat medical conditions that work in many different ways. One way is for the drug to bind to the active site of an enzyme. State the name given to the type of molecule that binds to the active site of an enzyme.

Figure 2

Naproxen has a chiral carbon, meaning that it exists as enantiomers.

i) Explain why only the correct enantiomer of Naproxen will be catalysed by a particular enzyme.

ii) Suggest why it is important for the patient taking the drug to the correct enantiomer.  

When the two amino acids, phenylalanine and serine, react together a dipeptide is formed.

Give the structural formula of the dipeptide formed when phenylalanine and serine react together.

When serine is at room temperature it exists as a solid. Name the type of compound that is formed and draw the displayed formula of the compound. 

Explain why amino acids such as serine are soluble in water and insoluble in organic solvents such as hydrocarbons.

The dipeptide formed from serine and phenylalanine is heated with concentration hydrochloric acid and a mixture of amino acids was formed. Thin Layer Chromatography (TLC) was used to separate the mixture.

i) Explain why a mixture of amino acids was formed.

ii) Outline briefly why TLC is able to separate these amino acids in this mixture.

Use your data sheet to answer the following questions

The amino acid alanine will react with excess chloromethane, draw the structure of the product formed in this reaction.

Alanine can also react with serine to produce two different dipeptides, draw both dipeptides formed in this reaction.

Explain the conditions in which alanine exists as a solid, draw the structure of the amino acid in these conditions.

Serine is a water soluble amino acid, whereas some amino acids are insoluble in water. Explain which part of the structure of an amino acid influences how soluble the molecule is in water. 

The tripeptide shown in Figure 1 is made of three different amino acid molecules. Draw the zwitterion of the central amino acid in the tripeptide shown.

Figure 1

Give the IUPAC name of the central amino acid in the tripeptide in part (a). 

Cysteine is included in the tripeptide shown in Figure 1 in part (a). Draw cysteine at a high pH.

Polypeptide chains are held together by hydrogen bonds. Draw a diagram to show how cysteine can form a different type of bond between polypeptide chains.

Explain how ‘R’ groups influence the structure of a tertiary protein.

A single strand of DNA is a polymer made up from four different monomers. DNA exists as two strands of nucleotides in the form of a double helix with hydrogen bonding between the strands.

Guanine and uracil are shown in Figure 1. Use the data sheet to draw a diagram to show how a molecule of guanine bonds with another molecule on the other strand of DNA.

Figure 1

Adenine forms a base pairing in RNA, explain how this pairing differs from your answer to part (a).

Explain why the bonding between adenine and it’s compatible base in RNA will bond in the same way as adenine’s compatible base in DNA.

The formula for urea is NH₂CONH₂ and when heated it can be used in alkaline conditions to separate the double helix structure of DNA.

Draw the displayed formula of urea and explain why the molecule can separate the DNA double helix. 

Isoleucine is shown in Figure 1 and has four stereoisomers. Draw each of the four stereoisomers in 3D representation.

Figure 1

Isoleucine can form a tripeptide with alanine and phenylalanine. State the maximum number of different tripeptide molecules can be formed from these three amino acids. Each tripeptide must have three different amino acids in.

The structure of the anticancer drug cisplatin is shown in Figure 2. Cisplatin was discovered in 1965 and is one of the most successful cancer treatments.

 Figure 2

Write an equation to show the formation of the complex produced when cisplatin enters the body and then reacts with water.

Draw a simplified diagram to show how cisplatin bonds with the DNA double helix.

In all living organisms a large variety of proteins are formed naturally from amino acids.

i) State the general formula of an amino acid

ii) Describe how amino acids can be combined to give a variety of polypeptides and proteins. 

Explain why DNA can behave as an acid. 

The amino acid proline is shown in Figure 1. Draw both dipeptides formed when proline reacts with phenylalanine.

Figure 1

Draw the product of the reaction between proline and ethanol in the presence of concentrated sulfuric acid.